Used extensively in bioconjugation, Cyanine3 NHS ester labels primary amine groups on proteins, peptides, and other biomolecules for fluorescence detection. It is commonly applied in fluorescence microscopy, flow cytometry, and immunostaining to visualize cellular components. Its bright orange-red fluorescence makes it ideal for multicolor imaging when paired with other fluorophores. The NHS ester group reacts efficiently with lysine residues and N-terminal amines under mild conditions, enabling labeling in aqueous buffers at near-neutral pH. It is also used in nucleic acid labeling when conjugated to amine-modified oligonucleotides for use in hybridization assays and microarray analysis.